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Phylogenetic tree

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Phylogenetic tree

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Not to be confused with Philogyny.

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A phylogenetic tree based on rRNA genes,[] showing the three life domains: bacteria, archaea, and eukaryota. The black branch at the bottom of the phylogenetic tree connects the three branches of living organisms to the last universal common ancestor. In the absence of an outgroup, the root is speculative.

A highly resolved, automatically generated tree of life, based on completely sequenced genomes.[1][2]

A phylogenetic tree (also phylogeny or evolutionary tree [3]) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry.

In a phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants,[] and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred.

Contents

1 History 2 Properties 2.1 Rooted tree 2.2 Unrooted tree

2.3 Bifurcating versus multifurcating

2.4 Labeled versus unlabeled

2.5 Enumerating trees

3 Special tree types

3.1 Dendrogram 3.2 Cladogram 3.3 Phylogram 3.4 Dahlgrenogram

3.5 Phylogenetic network

3.6 Spindle diagram 3.7 Coral of life 4 Construction 4.1 File formats

5 Limitations of phylogenetic analysis

6 See also 7 References 8 Further reading 9 External links 9.1 Images 9.2 General

History[edit]

The idea of a "tree of life" arose from ancient notions of a ladder-like progression from lower into higher forms of life (such as in the Great Chain of Being). Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book , by Edward Hitchcock (first edition: 1840).

Charles Darwin (1859) also produced one of the first illustrations and crucially popularized the notion of an evolutionary "tree" in his seminal book . Over a century later, evolutionary biologists still use tree diagrams to depict evolution because such diagrams effectively convey the concept that speciation occurs through the adaptive and semirandom splitting of lineages. Over time, species classification has become less static and more dynamic.

The term , or , derives from the two ancient greek words φῦλον (), meaning "race, lineage", and γένεσις (), meaning "origin, source".[4][5]

Properties[edit]

Rooted tree[edit]

Rooted phylogenetic tree optimized for blind people. The lowest point of the tree is the root, which symbolizes the universal common ancestor to all living beings. The tree branches out into three main groups: Bacteria (left branch, letters a to i), Archea (middle branch, letters j to p) and Eukaryota (right branch, letters q to z). Each letter corresponds to a group of organisms, listed below this description. These letters and the description should be converted to Braille font, and printed using a Braille printer. The figure can be 3D printed by copying the png file and using Cura or other software to generate the Gcode for 3D printing.

A rooted phylogenetic tree (see two graphics at top) is a directed tree with a unique node — the root — corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. The root node does not have a parent node, but serves as the parent of all other nodes in the tree. The root is therefore a node of degree 2, while other internal nodes have a minimum degree of 3 (where "degree" here refers to the total number of incoming and outgoing edges).

The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup.

Unrooted tree[edit]

Source : en.wikipedia.org

Understanding Evolutionary Trees

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

Original Science/Evolution Review

Open Access

Published: 12 February 2008

Understanding Evolutionary Trees

T. Ryan Gregory volume 1, pages

121–137 (2008)Cite this article

101k Accesses 106 Citations 130 Altmetric Metrics details

Abstract

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

Introduction: The Importance of Tree Thinking

In a flourish indicative of both his literary style and perceptive understanding of nature, Darwin (1859) offered the following arboreal metaphor to describe the diversification and extinction of species:

As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever-branching and beautiful ramifications.

Darwin clearly considered this Tree of Life as an important organizing principle in understanding the concept of “descent with modification” (what we now call evolution), having used a branching diagram of relatedness early in his exploration of the question (Fig. 1) and including a tree-like diagram as the only illustration in (Darwin 1859). Indeed, the depiction of historical relationships among living groups as a pattern of branching predates Darwin; Lamarck (1809), for example, used a similar type of illustration (see Gould 1999).

The first evolutionary tree sketched by Darwin (1837) in one of his notebooks. It is also of note that the only illustration in (Darwin 1859) was an evolutionary tree. Other early evolutionists before and after Darwin, including Lamarck (1809), also drew branching diagrams to indicate relatedness (see Gould 1999)

Full size image

Today, evolutionary trees are the subject of detailed, rigorous analysis that seeks to reconstruct the patterns of branching that have led to the diversity of life as we know it (e.g., Cracraft and Donoghue 2004; Hodkinson and Parnell 2007; Lecointre and Le Guyader 2007; Maddison and Schultz 2007). An entire discipline known as phylogenetics (Gr. , tribe + , birth) has emerged, complete with professional societies, dedicated scientific journals, and a complex technical literature that can be impenetrable to many nonspecialists. The output of this profession has become prodigious: It has been suggested that phylogeneticists as a group publish an average of 15 new evolutionary trees per day (Rokas 2006). Little surprise, then, that it has been argued that evolutionary biology as a whole has undergone a shift to “tree thinking” (O’Hara 1988), akin to the earlier movement toward “population thinking” that helped to shape the Neo-Darwinian synthesis around the mid-twentieth century (Mayr and Provine 1980).

Whereas tree thinking has permeated much of professional evolutionary biology, it has yet to exert its full influence among nonscientists. As Baum et al. (2005) recently pointed out, “Phylogenetic trees are the most direct representation of the principle of common ancestry—the very core of evolutionary theory—and thus they must find a more prominent place in the general public’s understanding of evolution.” In this regard, it is not so much the technical aspects of phylogenetic analysis

Footnote

1 that are of interest but a more practical understanding of what evolutionary trees represent and, at least as important, what they do not represent. As Baum et al. (2005) continued,

Tree thinking does not necessarily entail knowing how phylogenies are inferred by practicing systematists. Anyone who has looked into phylogenetics from outside the field of evolutionary biology knows that it is complex and rapidly changing, replete with a dense statistical literature, impassioned philosophical debates, and an abundance of highly technical computer programs. Fortunately, one can interpret trees and use them for organizing knowledge of biodiversity without knowing the details of phylogenetic inference.

Unfortunately, it is becoming clear that many readers lack a sufficient level of phylogenetic literacy to properly interpret evolutionary patterns and processes. For example, a recent study of undergraduate students who had received at least introductory instruction in evolutionary science revealed a range of common misconceptions about phylogenetic trees that represent “fundamental barriers to understanding how evolution operates” (Meir et al. 2007).

Source : evolution-outreach.biomedcentral.com

Phylogenetic trees

What a phylogenetic tree is. How to read phylogenetic trees and determine which species are most related.

Phylogeny

Phylogenetic trees

What a phylogenetic tree is. How to read phylogenetic trees and determine which species are most related.

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Key points:

A phylogenetic tree is a diagram that represents evolutionary relationships among organisms. Phylogenetic trees are hypotheses, not definitive facts.

The pattern of branching in a phylogenetic tree reflects how species or other groups evolved from a series of common ancestors.

In trees, two species are more related if they have a more recent common ancestor and less related if they have a less recent common ancestor.

Phylogenetic trees can be drawn in various equivalent styles. Rotating a tree about its branch points doesn't change the information it carries.

Introduction

Humans as a group are big on organizing things. Not necessarily things like closets or rooms; I personally score low on the organization front for both of those things. Instead, people often like to group and order the things they see in the world around them. Starting with the Greek philosopher Aristotle, this desire to classify has extended to the many and diverse living things of Earth.

Most modern systems of classification are based on evolutionary relationships among organisms – that is, on the organisms’ phylogeny. Classification systems based on phylogeny organize species or other groups in ways that reflect our understanding of how they evolved from their common ancestors.

In this article, we'll take a look at phylogenetic trees, diagrams that represent evolutionary relationships among organisms. We'll see exactly what we can (and can't!) infer from a phylogenetic tree, as well as what it means for organisms to be more or less related in the context of these trees.

Anatomy of a phylogenetic tree

When we draw a phylogenetic tree, we are representing our best hypothesis about how a set of species (or other groups) evolved from a common ancestor

^1 1

start superscript, 1, end superscript

. As we'll explore further in the article on building trees, this hypothesis is based on information we’ve collected about our set of species – things like their physical features and the DNA sequences of their genes.

[Are phylogenetic trees only for species?]

In a phylogenetic tree, the species or groups of interest are found at the tips of lines referred to as the tree's branches. For example, the phylogenetic tree below represents relationships between five species, A, B, C, D, and E, which are positioned at the ends of the branches:

Image modified from Taxonomy and phylogeny: Figure 2 by Robert Bear et al., CC BY 4.0

The pattern in which the branches connect represents our understanding of how the species in the tree evolved from a series of common ancestors. Each branch point (also called an internal node) represents a divergence event, or splitting apart of a single group into two descendant groups.

At each branch point lies the most recent common ancestor of all the groups descended from that branch point. For instance, at the branch point giving rise to species A and B, we would find the most recent common ancestor of those two species. At the branch point right above the root of the tree, we would find the most recent common ancestor of all the species in the tree (A, B, C, D, E). [Why is this the most recent common ancestor of all the species?]

Image modified from Taxonomy and phylogeny: Figure 2 by Robert Bear et al., CC BY 4.0

Each horizontal line in our tree represents a series of ancestors, leading up to the species at its end. For instance, the line leading up to species E represents the species' ancestors since it diverged from the other species in the tree. Similarly, the root represents a series of ancestors leading up to the most recent common ancestor of all the species in the tree.

Which species are more related?

In a phylogenetic tree, the relatedness of two species has a very specific meaning. Two species are more related if they have a more recent common ancestor, and less related if they have a less recent common ancestor.

We can use a pretty straightforward method to find the most recent common ancestor of any pair or group of species. In this method, we start at the branch ends carrying the two species of interest and “walk backwards” in the tree until we find the point where the species’ lines converge.

For instance, suppose that we wanted to say whether A and B or B and C are more closely related. To do so, we would follow the lines of both pairs of species backward in the tree. Since A and B converge at a common ancestor first as we move backwards, and B only converges with C after its junction point with A, we can say that A and B are more related than B and C.

Source : www.khanacademy.org